rs1728400

Variant names:

• chr16-86400840-C-A
• rs1728400

Your query was ambiguous. Multiple possible variants found:

• chr16-86400840-C-A
• chr16-86400840-C-G
• chr16-86400840-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.586 in 152,092 control chromosomes in the GnomAD database, including 29,361 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (29361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89052 AN: 151974 Hom.: 29317 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.602

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.586 AC: 89147 AN: 152092 Hom.: 29361 Cov.: 32 AF XY: 0.580 AC XY: 43107 AN XY: 74342

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.598

Alfa AF: 0.475 Hom.: 35668

Bravo AF: 0.616

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1728400; hg19: chr16-86434446;